Re-evaluation of the inheritance for root-knot nematode resistance in the Upland cotton germplasm line M-120 RNR revealed two epistatic QTLs conferring resistance

Evaluation of Meloidogyne Incognita and Rotylenchulus Reniformis Nematode-resistant Cotton Cultivars with Supplemental Corteva Agriscience Nematicides

Meloidogyne incognita- and Rotylenchulus reniformis-resistant new cotton cultivars have recently become available, giving growers a new option in nematode management. The objectives of this study were: (i) to determine the yield potential of the new cultivars PHY 360 W3FE (M. incognita-resistant) and PHY 332 W3FE (R. reniformis-resistant) in nematode-infested fields and (ii) to evaluate the effects of combining the nematicides Reklemel (fluazaindolizine), Vydate C-LV (oxamyl), and the seed treatment BIOST Nematicide 100 (heat killed Burkholderia rinojenses and its non-living spent fermentation media) with resistant cotton cultivars on nematode population levels and lint yield. Field experiments in 2020 and 2021 indicated M. incognita population levels were 73% lower on PHY 360 W3FE (R) and 80% lower for R. reniformis on the PHY 332 W3FE (R) at 40 days after planting. Nematode eggs per gram of root were further reduced an average of 86% after the addition of Reklemel and Vydate C-LV when averaging both cultivars over the two years. Tests with BIOST Nematicide 100 + Reklemel + Vydate C-LV (0.56 + 2.5 L/ha) in both M. incognita and R. reniformis fields produced higher lint yields. Overall, planting PHY 360 W3FE (R) and PHY 332 W3FE (R) improved yields an average of 364 kg/ha while limiting nematode population increases. The addition of the nematicides further increased yields 152 kg/ha of the nematode-resistant cultivars.

A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance

A major QTL conferring resistance to Fusarium wilt race 4 in a narrow region of chromosome D02 was identified in a MAGIC population of 550 RILs of Upland cotton. Numerous studies have been conducted to investigate the genetic basis of Fusarium wilt (FW, caused by Fusarium oxysporum f. sp. vasinfectum, FOV) resistance using bi-parental and association mapping populations in cotton. In this study, a multi-parent advanced generation inter-cross (MAGIC) population of 550 recombinant inbred lines (RILs), together with their 11 Upland cotton (Gossypium hirsutum) parents, was used to identify QTLs for FOV race 4 (FOV4) resistance. Among the parents, Acala Ultima, M-240 RNR, and Stoneville 474 were the most resistant, while Deltapine Acala 90, Coker 315, and Stoneville 825 were the most susceptible. Twenty-two MAGIC lines were consistently resistant to FOV4. Through a genome-wide association study (GWAS) based on 473,516 polymorphic SNPs, a major FOV4 resistance QTL within a narrow region on chromosomes D02 was detected, allowing identification of 14 candidate genes. Additionally, a meta-analysis of 133 published FW resistance QTLs showed a D subgenome and individual chromosome bias and no correlation between homeologous chromosome pairs. This study represents the first GWAS study using a largest genetic population and the most comprehensive meta-analysis for FW resistance in cotton. The results illustrated that 550 lines were not enough for high resolution mapping to pinpoint a candidate gene, and experimental errors in phenotyping cotton for FW resistance further compromised the accuracy and precision in QTL localization and identification of candidate genes. This study identified FOV4-resistant parents and MAGIC lines, and the first major QTL for FOV4 resistance in Upland cotton, providing useful information for developing FOV4-resistant cultivars and further genomic studies towards identification of causal genes for FOV4 resistance in cotton.

QTL mapping for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.)

The resistance to cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.) was studied using 114 doubled haploid lines from a novel ITMI mapping population. These lines were screened for nematode infestation in a controlled environment for two years. QTL-mapping analyses were performed across two years (Y1 and Y2) as well as combining two years (CY) data. On the 114 lines that were screened, a total of 2,736 data points (genotype, batch or years, and replication combinations) were acquired. For QTL analysis, 12,093 markers (11,678 SNPs and 415 SSRs markers) were used, after filtering the genotypic data, for the QTL mapping. Composite interval mapping, using Haley-Knott regression (hk) method in R/QTL, was used for QTL analysis. In total, 19 QTLs were detected out of which 13 were novel and six were found to be colocalized or nearby to previously reported Cre genes, QTLs or MTAs for H. avenae or H. filipjevi. Nine QTLs were detected across all three groups (Y1, Y2 and CY) including a significant QTL "QCcn.ha-2D" on chromosome 2D that explains 23% of the variance. This QTL colocalized with a previously identified Cre3 locus. Novel QTL, QCcn.ha-2A, detected in the present study could be the possible unreported homeoloci to QCcn.ha-2D, QCcn.ha-2B.1 and QCcn.ha-2B.2. Six significant digenic epistatic interactions were also observed. In addition, 26 candidate genes were also identified including genes known for their involvement in PPNs (plant parasitic nematodes) resistance in different plant species. In-silico expression of putative candidate genes showed differential expression in roots during specific developmental stages. Results obtained in the present study are useful for wheat breeding to generate resistant genetic resources against H. avenae.

Root-Knot Nematode Resistance in Gossypium hirsutum Determined by a Constitutive Defense-Response Transcriptional Program Avoiding a Fitness Penalty

Cotton (Gossypium spp.) is the most important renewable source of natural textile fiber and one of the most cultivated crops around the world. Plant-parasitic nematode infestations, such as the southern Root-Knot Nematode (RKN) Meloidogyne incognita, represent a threat to cotton production worldwide. Host-plant resistance is a highly effective strategy to manage RKN; however, the underlying molecular mechanisms of RKN-resistance remain largely unknown. In this study, we harness the differences in RKN-resistance between a susceptible (Acala SJ-2, SJ2), a moderately resistant (Upland Wild Mexico Jack Jones, WMJJ), and a resistant (Acala NemX) cotton entries, to perform genome-wide comparative analysis of the root transcriptional response to M. incognita infection. RNA-seq data suggest that RKN-resistance is determined by a constitutive state of defense transcriptional behavior that prevails in the roots of the NemX cultivar. Gene ontology and protein homology analyses indicate that the root transcriptional landscape in response to RKN-infection is enriched for responses related to jasmonic and salicylic acid, two key phytohormones in plant defense responses. These responses are constitutively activated in NemX and correlate with elevated levels of these two hormones while avoiding a fitness penalty. We show that the expression of cotton genes coding for disease resistance and receptor proteins linked to RKN-resistance and perception in plants, is enhanced in the roots of RKN-resistant NemX. Members of the later gene families, located in the confidence interval of a previously identified QTL associated with RKN resistance, represent promising candidates that might facilitate introduction of RKN-resistance into valuable commercial varieties of cotton. Our study provides novel insights into the molecular mechanisms that underlie RKN resistance in cotton.

The effect of two QTLs for resistance to Meloidogyne incognita in cotton on nematode egression from roots

Cotton is widely grown in the southern US and Meloidogyne incognita is its most significant pathogen. The germplasm line M-120 RNR is highly resistant to M. incognita due to two resistance QTLs (quantitative trait loci), qMi-C11 and qMi-C14. Both QTLs reduce total egg production, but the QTLs affect M. incognita development at different life stages. The QTLs do not appear to affect initial penetration of M. incognita but genotypes containing qMi-C11 had fewer nematodes in the roots 8 days after inoculation than near isolines without qMi-C11, which may indicate M. incognita egression from roots. Three greenhouse trials were conducted using cotton isolines to determine whether qMi-C11 and qMi-C14 affect egression of M. incognita juveniles from roots. On each of the five sampling dates (4, 6, 8, 10, and 12 DAI), nematodes that egressed from roots were counted and roots were stained to count nematodes that remained in the roots. The effect of resistance QTLs on M. incognita egression from the roots differed among the trials. Nematode egression was consistently numerically greater, but inconsistently statistically different, from plants with both QTLs than from plants with neither QTL. Plants with only one QTL generally did not differ from plants with both QTLs, and the effects of qMi-C11 and qMi-C14 did not differ in any consistent way. In a separate experiment, plants with neither QTL had more eggs per egg mass than did plants with both QTLs, whereas plants with only one QTL had an intermediate number. Root gall size was measured in two trials and no consistent differences in gall size were observed. We conclude that (1) qMi-C11 and qMi-C14 do not stimulate nematode egression from cotton roots, (2) both qMi-C11 and qMi-C14 reduce M. incognita eggs/egg mass, and (3) neither qMi-C11 nor qMi-C14 affect gall size.

Analysis of Cotton Chromosome 11 and 14 Root-Knot Nematode Resistance Quantitative Trait Loci Effects on Root-Knot Nematode Postinfection Development, Egg Mass Formation, and Fecundity

Cotton (Gossypium hirsutum) resistance to root-knot nematode (RKN) (Meloidogyne incognita) is controlled by quantitative trait loci (QTLs) on chromosomes 11 (CHR11) and 14 (CHR14). The individual contributions of these QTLs to resistance are not completely understood. We developed near isogenic lines susceptible at both loci (null), having CHR11 or CHR14 alone, and having both QTLs (CHR11/CHR14). RKN reproduction, postinfection development, egg mass formation, and adult female fecundity were evaluated. Total RKN reproduction was reduced more in CHR14 versus CHR11 but not as greatly as in CHR11/CHR14. Second-stage juvenile (J2) development to the J3 and J4 (J3+J4) life stages was delayed in CHR11, whereas the J2 transition to J3+J4 in CHR14 followed a similar track as in null plants. Development of J3+J4 nematodes to adult females was inhibited in CHR14 at 21 days after inoculation (DAI). Adult female numbers were decreased in CHR11 and CHR14 at 21 and 28 DAI, with CHR11/CHR14 showing an even greater reduction by 28 DAI. The number of egg masses per gram of root at 21, 28, and 35 DAI formed on CHR11 and CHR14 followed a similar track as numbers of adult females. RKN adult female fecundity (eggs/egg mass) was reduced for CHR11 and CHR14 compared with the null at 21 DAI; however, CHR11 eggs/egg mass was only slightly reduced versus the null by 28 DAI. In contrast, CHR14 eggs/egg mass was like CHR11/CHR14, showing a 4-fold decrease compared with CHR11 and the null.

Sequence Composition of Bacterial Chromosome Clones in a Transgressive Root-Knot Nematode Resistance Chromosome Region in Tetraploid Cotton

Plants evolve innate immunity including resistance genes to defend against pest and pathogen attack. Our previous studies in cotton (Gossypium spp.) revealed that one telomeric segment on chromosome (Chr) 11 in G. hirsutum cv. Acala NemX (rkn1 locus) contributed to transgressive resistance to the plant parasitic nematode Meloidogyne incognita, but the highly homologous segment on homoeologous Chr 21 had no resistance contribution. To better understand the resistance mechanism, a bacterial chromosome (BAC) library of Acala N901 (Acala NemX resistance source) was used to select, sequence, and analyze BAC clones associated with SSR markers in the complex rkn1 resistance region. Sequence alignment with the susceptible G. hirsutum cv. TM-1 genome indicated that 23 BACs mapped to TM-1-Chr11 and 18 BACs mapped to TM-1-Chr 21. Genetic and physical mapping confirmed less BAC sequence (53-84%) mapped with the TM-1 genome in the rkn1 region on Chr 11 than to the homologous region (>89%) on Chr 21. A 3.1-cM genetic distance between the rkn1 flanking markers CIR316 and CIR069 was mapped in a Pima S-7 × Acala NemX RIL population with a physical distance ∼1 Mbp in TM-1. NCBI Blast and Gene annotation indicated that both Chr 11 and Chr 21 harbor resistance gene-rich cluster regions, but more multiple homologous copies of Resistance (R) proteins and of adjacent transposable elements (TE) are present within Chr 11 than within Chr 21. (CC)-NB-LRR type R proteins were found in the rkn1 region close to CIR316, and (TIR)-NB-LRR type R proteins were identified in another resistance rich region 10 cM from CIR 316 (∼3.1 Mbp in the TM-1 genome). The identified unique insertion/deletion in NB-ARC domain, different copies of LRR domain, multiple copies or duplication of R proteins, adjacent protein kinases, or TE in the rkn1 region on Chr 11 might be major factors contributing to complex recombination and transgressive resistance.

Transcriptome analysis of a nematode resistant and susceptible upland cotton line at two critical stages of Meloidogyne incognita infection and development

Host plant resistance is the most practical approach to control the Southern root-knot nematode (Meloidogyne incognita; RKN), which has emerged as one of the most serious economic pests of Upland cotton (Gossypium hirsutum L.). Previous QTL analyses have identified a resistance locus on chromosome 11 (qMi-C11) affecting galling and another locus on chromosome-14 (qMi-C14) affecting egg production. Although these two QTL regions were fine mapped and candidate genes identified, expression profiling of genes would assist in further narrowing the list of candidate genes in the QTL regions. We applied the comparative transcriptomic approach to compare expression profiles of genes between RKN susceptible and resistance genotypes at an early stage of RKN development that coincides with the establishment of a feeding site and at the late stage of RKN development that coincides with RKN egg production. Sequencing of cDNA libraries produced over 315 million reads of which 240 million reads (76%) were mapped on to the Gossypium hirsutum genome. A total of 3,789 differentially expressed genes (DEGs) were identified which were further grouped into four clusters based on their expression profiles. A large number of DEGs were found to be down regulated in the susceptible genotype at the late stage of RKN development whereas several genes were up regulated in the resistant genotype. Key enriched categories included transcription factor activity, defense response, response to phyto-hormones, cell wall organization, and protein serine/threonine kinase activity. Our results also show that the DEGs in the resistant genotype at qMi-C11 and qMi-C14 loci displayed higher expression of defense response, detoxification and callose deposition genes, than the DEGs in the susceptible genotype.

Resistance Quantitative Trait Loci qMi-C11 and qMi-C14 in Cotton Have Different Effects on the Development of Meloidogyne incognita, the Southern Root-Knot Nematode

Quantitative trait loci (QTLs) qMi-C11 and qMi-C14 impart a high level of resistance to Meloidogyne incognita in cotton. Breeders had previously backcrossed both QTLs into the susceptible Coker 201 to create the highly resistant M-120 RNR, and we crossed Coker 201 and M-120 RNR to create near-isogenic lines with either qMi-C11 or qMi-C14. Previous work suggests different modes of action for qMi-C11 and qMi-C14. To document individual and combined effects of the QTLs on nematode development and reproduction, Coker 201 (neither QTL), M-120 RNR (both QTLs), CH11 near isoline (qMi-C11), and CH14 near isoline (qMi-C14) were inoculated with M. incognita. At 4, 8, 12, 16, 20, 25, and 30 days after inoculation (DAI), roots were stained to observe nematode developmental stages (second-stage juvenile [J2], swollen second-stage juvenile [SJ2], third-stage juvenile [J3], fourth-stage juvenile [J4], and female), and the number of galls was counted. At 20, 25, 30, and 40 DAI, M. incognita eggs were harvested and counted. At 30 DAI, 80% of the nematodes on Coker 201 were female compared with 50, 40, and 33% females on CH14, CH11, and M-120 RNR, respectively, and greater proportions of nematodes remained in J2 in M-120 RNR (41%), CH11 (58%), and CH14 (27%) than in Coker 201 (9%). More nematodes progressed to J3 or J4 on Coker 201 and CH14 than on CH11 or M-120 RNR. Coker 201 and CH14 had more galls than M-120 RNR. Coker 201 had more eggs than the other genotypes at 30 DAI. Nematode development beyond J2 or SJ2 was significantly reduced by qMi-C11, and development beyond J3 or J4 was significantly reduced by qMi-C14. This study confirms that qMi-C11 and qMi-C14 act at different times and have different effects on the development of M. incognita, and therefore, they have different modes of action.

A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 (D02) in Upland cotton

MAGIC population sequencing and virus-induced gene silencing identify Gh_D02G0276 as a novel root-knot nematode resistance gene on chromosome 14 in Upland cotton. The southern root-knot nematode [RKN; Meloidogyne incognita (Kofoid & White)] remains the primary yield-limiting biotic stress to Upland cotton (Gossypium hirsutum L.) throughout the southeastern USA. While useful genetic markers have been developed for two major RKN resistance loci on chromosomes 11 (A11) and 14 (D02), these markers are not completely effective because the causative genes have not been identified. Here, we sequenced 550 recombinant inbred lines (RILs) from a multi-parent advanced generation intercross (MAGIC) population to identify five RILs that had informative recombinations near the D02-RKN resistance locus. The RKN resistance phenotypes of these five RILs narrowed the D02-RKN locus to a 30-kb region with four candidate genes. We conducted virus-induced gene silencing (VIGS) on each of these genes and found that Gh_D02G0276 was required for suppression of RKN egg production conferred by the Chr. D02 resistance gene. The resistant lines all possessed an allele of Gh_D02G0276 that showed non-synonymous mutations and was prematurely truncated. Furthermore, a Gh_D02G0276-specific marker for the resistance allele variant was able to identify RKN-resistant germplasm from a collection of 367 cotton accessions. The Gh_D02G0276 peptide shares similarity with domesticated hAT-like transposases with additional novel N- and C-terminal domains that resemble the target of known RKN effector molecules and a prokaryotic motif, respectively. The truncation in the resistance allele results in a loss of a plant nuclear gene-specific C-terminal motif, potentially rendering this domain antigenic due to its high homology with bacterial proteins. The conclusive identification of this RKN resistance gene opens new avenues for understanding plant resistance mechanisms to RKN as well as opportunities to develop more efficient marker-assisted selection in cotton breeding programs.

Quantitative trait loci mapping of Meloidogyne incognita and M. hapla resistance in a recombinant inbred line population of soybean

A recombinant inbred line population of soybean (Glycine max) was utilised to identify the quantitative trait loci (QTLs) determining the response to infection by two root-knot nematode species, Meloidogyne incognita and M. hapla, in glasshouse assays. QTL analysis detected seven major and four minor QTLs on seven soybean chromosomes ((Chrs) 1, 7, 8, 10, 14, 18, 20) explaining 6-41% phenotypic variance (PVE) for M. incognita root response and nematode reproduction. Three of the major QTLs, on Chrs 7, 10 and 18, were confirmed in previous reports and two major QTLs on Chrs 14 and 20 were detected for the first time. The QTL analysis with M. hapla provides the first report of a major QTL region mapped on Chr 7, explaining 70-82% PVE in M. hapla root response and nematode reproduction. These novel identified QTLs with flanking markers will be helpful in marker-assisted breeding for nematode resistance in soybean.

QTL Analysis of Transgressive Nematode Resistance in Tetraploid Cotton Reveals Complex Interactions in Chromosome 11 Regions

Transgressive segregation in cotton (Gossypium spp.) provides an important approach to enhance resistance to the major pest root-knot nematode (RKN) Meloidogyne incognita. Our previous studies reported transgressive RKN resistance in an intraspecific Gossypium hirsutum resistant NemX × susceptible SJ-2 recombinant inbred line (RIL) population and early generations of interspecific cross Gossypium barbadense (susceptible Pima S-7) × G. hirsutum (NemX). However, the underlying functional mechanisms for this phenomenon are not known. In this study, the region of RKN resistance gene rkn1 on chromosome (Chr) 11 and its homoeologous Chr 21 was fine mapped with G. raimondii D₅ genome reference sequence. Transgressive resistance was found in the later generation of a new RIL population F_2:7 (Pima S-7 × NemX) and one interspecific F₂ (susceptible Pima S-7 × susceptible SJ-2). QTL analysis revealed similar contributions to root-galling and egg-production resistance phenotypes associated with SSR marker CIR316 linked to resistance gene rkn1 in NemX on Chr 11 in all seven populations analyzed. In testcross NemX × F₁ (Pima S-7 × SJ-2) marker allele CIR069-271 from Pima S-7 linked to CIR316 contributed 63% of resistance to galling phenotype in the presence of rkn1. Similarly, in RIL population F_2:8 (NemX × SJ-2), SJ-2 markers closely linked to CIR316 contributed up to 82% of resistance to root-galling. These results were confirmed in BC₁F₁ SJ-2 × F₁ (NemX × SJ-2), F₂ (NemX × SJ-2), and F₂ (Pima S-7 × SJ-2) populations in which up to 44, 36, and 15% contribution in resistance to galling was found, respectively. Transgressive segregation for resistance was universal in all intra- and inter-specific populations, although stronger transgressive resistance occurred in later than in early generations in the intraspecific cross compared with the interspecific cross. Transgressive effects on progeny from susceptible parents are possibly provided in the rkn1 resistance region of chromosome 11 by tandemly arrayed allele (TAA) or gene (TAG) interactions contributing to transgressive resistance. Complex TAA and TAG recombination and interactions in the rkn1 resistance region provide three genes and a model to study disease and transgressive resistance in polyploid plants, and novel genotypes for plant breeding.

Coupling of MIC-3 overexpression with the chromosomes 11 and 14 root-knot nematode (RKN) (Meloidogyne incognita) resistance QTLs provides insights into the regulation of the RKN resistance response in Upland cotton (Gossypium hirsutum)

Genetic analysis of MIC-3 transgene with RKN resistance QTLs provides insight into the resistance regulatory mechanism and provides a framework for testing additional hypotheses. Resistance to root-knot nematode (RKN) (Meloidogyne incognita) in Upland cotton (Gossypium hirsutum) is mediated by two major quantitative trait loci (QTL) located on chromosomes 11 and 14. The MIC-3 (Meloidogyne Induced Cotton3) protein accumulates specifically within the immature galls of RKN-resistant plants that possess these QTLs. Recently, we showed that MIC-3 overexpression in an RKN-susceptible cotton genotype suppressed RKN egg production but not RKN-induced root galling. In this study, the MIC-3 overexpression construct T-DNA in the single-copy transgenic line '14-7-1' was converted into a codominant molecular marker that allowed the marker assisted selection of F2:3 cotton lines, derived from a cross between 14-7-1 and M-240 RNR, having all possible combinations of the chromosomes 11 and 14 QTLs with and without the MIC-3 overexpression construct. Root-knot nematode reproduction (eggs g(-1) root) and severity of RKN-induced root galling were assessed in these lines. We discovered that the addition of MIC-3 overexpression suppressed RKN reproduction in lines lacking both resistance QTLs and in lines having only the chromosome 14 QTL, suggesting an additive effect of the MIC-3 construct with this QTL. In contrast, MIC-3 overexpression did not improve resistance in lines having the single chromosome 11 QTL or in lines having both resistance QTLs, suggesting an epistatic interaction between the chromosome 11 QTL and the MIC-3 construct. Overexpression of MIC-3 did not affect the severity of RKN-induced root galling regardless of QTL genotype. These data provide new insights into the relative order of action of the chromosomes 11 and 14 QTLs and their potential roles in regulating MIC-3 expression as part of the RKN resistance response.

Fine mapping and identification of candidate genes for a QTL affecting Meloidogyne incognita reproduction in Upland cotton

Background

The southern root-knot nematode (Meloidogyne incognita; RKN) is one of the most important economic pests of Upland cotton (Gossypium hirsutum L.). Host plant resistance, the ability of a plant to suppress nematode reproduction, is the most economical, practical, and environmentally sound method to provide protection against this subterranean pest. The resistant line Auburn 623RNR and a number of elite breeding lines derived from it remain the most important source of root-knot nematode (RKN) resistance. Prior genetic analysis has identified two epistatically interacting RKN resistance QTLs, qMi-C11 and qMi-C14, affecting gall formation and RKN reproduction, respectively.

Results

We developed a genetic population segregating only for the qMi-C14 locus and evaluated the genetic effects of this QTL on RKN resistance in the absence of the qMi-C11 locus. The qMi-C14 locus had a LOD score of 12 and accounted for 24.5 % of total phenotypic variation for egg production. In addition to not being significantly associated with gall formation, this locus had a lower main effect on RKN reproduction than found in our previous study, which lends further support to evidence of epistasis with qMi-C11 in imparting RKN resistance in the Auburn 623RNR source. The locus qMi-C14 was fine-mapped with the addition of 16 newly developed markers. By using the reference genome sequence of G. raimondii, we identified 20 candidate genes encoding disease resistance protein homologs in the newly defined 2.3 Mb region flanked by two SSR markers. Resequencing of an RKN resistant and susceptible G. hirsutum germplasm revealed non-synonymous mutations in only four of the coding regions of candidate genes, and these four genes are consequently of high interest.

Conclusions

Our mapping results validated the effects of the qMi-C14 resistance locus, delimiting the QTL to a smaller region, and identified tightly linked SSR markers to improve the efficiency of marker-assisted selection. The candidate genes identified warrant functional studies that will help in identifying and characterizing the actual qMi-C14 defense gene(s) against root-knot nematodes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2954-1) contains supplementary material, which is available to authorized users.

Reproduction of Meloidogyne incognita Race 3 on Flue-cured Tobacco Homozygous for Rk1 and/or Rk2 Resistance Genes

Most commercial tobacco cultivars possess the Rk1 resistance gene to races 1 and 3 of Meloidogyne incognita and race 1 of Meloidogyne arenaria, which has caused a shift in population prevalence in Virginia tobacco fields toward other species and races. A number of cultivars now also possess the Rk2 gene for root-knot resistance. Experiments were conducted in 2013 to 2014 to examine whether possessing both Rk1 and Rk2 increases resistance to a variant of M. incognita race 3 compared to either gene alone. Greenhouse trials were arranged in a completely randomized design with Coker 371-Gold (C371G; susceptible), NC 95 and SC 72 (Rk1Rk1), T-15-1-1 (Rk2Rk2), and STNCB-2-28 and NOD 8 (Rk1Rk1 and Rk2Rk2). Each plant was inoculated with 5,000 root-knot nematode eggs; data were collected 60 d postinoculation. Percent galling and numbers of egg masses and eggs were counted, the latter being used to calculate the reproductive index on each host. Despite variability, entries with both Rk1 and Rk2 conferred greater resistance to a variant of M. incognita race 3 than plants with Rk1 or Rk2 alone. Entries with Rk1 alone were successful in reducing root galling and nematode reproduction compared to the susceptible control. Entry T-15-1-1 did not reduce galling compared to the susceptible control but often suppressed reproduction.

Plant Genetic Background Increasing the Efficiency and Durability of Major Resistance Genes to Root-knot Nematodes Can Be Resolved into a Few Resistance QTLs

With the banning of most chemical nematicides, the control of root-knot nematodes (RKNs) in vegetable crops is now based essentially on the deployment of single, major resistance genes (R-genes). However, these genes are rare and their efficacy is threatened by the capacity of RKNs to adapt. In pepper, several dominant R-genes are effective against RKNs, and their efficacy and durability have been shown to be greater in a partially resistant genetic background. However, the genetic determinants of this partial resistance were unknown. Here, a quantitative trait loci (QTL) analysis was performed on the F2:3 population from the cross between Yolo Wonder, an accession considered partially resistant or resistant, depending on the RKN species, and Doux Long des Landes, a susceptible cultivar. A genetic linkage map was constructed from 130 F2 individuals, and the 130 F3 families were tested for resistance to the three main RKN species, Meloidogyne incognita, M. arenaria, and M. javanica. For the first time in the pepper-RKN pathosystem, four major QTLs were identified and mapped to two clusters. The cluster on chromosome P1 includes three tightly linked QTLs with specific effects against individual RKN species. The fourth QTL, providing specific resistance to M. javanica, mapped to pepper chromosome P9, which is known to carry multiple NBS-LRR repeats, together with major R-genes for resistance to nematodes and other pathogens. The newly discovered cluster on chromosome P1 has a broad spectrum of action with major additive effects on resistance. These data highlight the role of host QTLs involved in plant-RKN interactions and provide innovative potential for the breeding of new pepper cultivars or rootstocks combining quantitative resistance and major R-genes, to increase both the efficacy and durability of RKN control by resistance genes.

Genetic analysis of Verticillium wilt resistance in a backcross inbred line population and a meta-analysis of quantitative trait loci for disease resistance in cotton

Background

Verticillium wilt (VW) and Fusarium wilt (FW), caused by the soil-borne fungi Verticillium dahliae and Fusarium oxysporum f. sp. vasinfectum, respectively, are two most destructive diseases in cotton production worldwide. Root-knot nematodes (Meloidogyne incognita, RKN) and reniform nematodes (Rotylenchulus reniformis, RN) cause the highest yield loss in the U.S. Planting disease resistant cultivars is the most cost effective control method. Numerous studies have reported mapping of quantitative trait loci (QTLs) for disease resistance in cotton; however, very few reliable QTLs were identified for use in genomic research and breeding.

Results

This study first performed a 4-year replicated test of a backcross inbred line (BIL) population for VW resistance, and 10 resistance QTLs were mapped based on a 2895 cM linkage map with 392 SSR markers. The 10 VW QTLs were then placed to a consensus linkage map with other 182 VW QTLs, 75 RKN QTLs, 27 FW QTLs, and 7 RN QTLs reported from 32 publications. A meta-analysis of QTLs identified 28 QTL clusters including 13, 8 and 3 QTL hotspots for resistance to VW, RKN and FW, respectively. The number of QTLs and QTL clusters on chromosomes especially in the A-subgenome was significantly correlated with the number of nucleotide-binding site (NBS) genes, and the distribution of QTLs between homeologous A- and D- subgenome chromosomes was also significantly correlated.

Conclusions

Ten VW resistance QTL identified in a 4-year replicated study have added useful information to the understanding of the genetic basis of VW resistance in cotton. Twenty-eight disease resistance QTL clusters and 24 hotspots identified from a total of 306 QTLs and linked SSR markers provide important information for marker-assisted selection and high resolution mapping of resistance QTLs and genes. The non-overlapping of most resistance QTL hotspots for different diseases indicates that their resistances are controlled by different genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1682-2) contains supplementary material, which is available to authorized users.

Overexpression of MIC-3 indicates a direct role for the MIC gene family in mediating Upland cotton (Gossypium hirsutum) resistance to root-knot nematode (Meloidogyne incognita)

Transgene-based analysis of the MIC-3 gene provides the first report of a cotton gene having a direct role in mediating cotton resistance to root-knot nematode. Major quantitative trait loci have been mapped to Upland cotton (Gossypium hirsutum L.) chromosomes 11 and 14 that govern the highly resistant phenotype in response to infection by root-knot nematode (RKN; Meloidogyne incognita); however, nearly nothing is known regarding the underlying molecular determinants of this RKN-resistant phenotype. Multiple lines of circumstantial evidence have strongly suggested that the MIC (Meloidogyne Induced Cotton) gene family plays an integral role in mediating cotton resistance to RKN. In this report, we demonstrate that overexpression of MIC-3 in the RKN-susceptible genetic background Coker 312 reduces RKN egg production by ca. 60-75 % compared to non-transgenic controls and transgene-null sibling lines. MIC-3 transcript and protein overexpression were confirmed in root tissues of multiple independent transgenic lines with each line showing a similar level of increased resistance to RKN. In contrast to RKN fecundity, transgenic lines showed RKN-induced root galling similar to the susceptible controls. In addition, we determined that this effect of MIC-3 overexpression was specific to RKN as no effect was observed on reniform nematode (Rotylenchulus reniformis) reproduction. Transgenic lines did not show obvious alterations in growth, morphology, flowering, or fiber quality traits. Gene expression analyses showed that MIC-3 transcript levels in uninfected transgenic roots exceeded levels observed in RKN-infected roots of naturally resistant plants and that overexpression did not alter the regulation of native MIC genes in the genome. These results are the first report describing a direct role for a specific gene family in mediating cotton resistance to a plant-parasitic nematode.